ADAPTABLE: a comprehensive web platform of antimicrobial peptides tailored to the user’s research

Ramos‐Martín, Francisco; Annaval, Thibault; Buchoux, Sébastien; Sarazin, Catherine; D’Amelio, Nicola

doi:10.26508/lsa.201900512

Cited by 33 publications

(28 citation statements)

References 88 publications

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“…The work was organized as follows. First, property-alignment [ 38 ] was used to highlight important motifs along the sequence and to explore further possible activities of K11. Second, we studied the structure of the peptide in solution and in the presence of simple biomimetic models (micelles and isotropic bicelles).…”

Section: Resultsmentioning

confidence: 99%

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Antimicrobial Peptide K11 Selectively Recognizes Bacterial Biomimetic Membranes and Acts by Twisting Their Bilayers

et al. 2020

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K11 is a synthetic peptide originating from the introduction of a lysine residue in position 11 within the sequence of a rationally designed antibacterial scaffold. Despite its remarkable antibacterial properties towards many ESKAPE bacteria and its optimal therapeutic index (320), a detailed description of its mechanism of action is missing. As most antimicrobial peptides act by destabilizing the membranes of the target organisms, we investigated the interaction of K11 with biomimetic membranes of various phospholipid compositions by liquid and solid-state NMR. Our data show that K11 can selectively destabilize bacterial biomimetic membranes and torque the surface of their bilayers. The same is observed for membranes containing other negatively charged phospholipids which might suggest additional biological activities. Molecular dynamic simulations reveal that K11 can penetrate the membrane in four steps: after binding to phosphate groups by means of the lysine residue at the N-terminus (anchoring), three couples of lysine residues act subsequently to exert a torque in the membrane (twisting) which allows the insertion of aromatic side chains at both termini (insertion) eventually leading to the flip of the amphipathic helix inside the bilayer core (helix flip and internalization).

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Section: Resultsmentioning

confidence: 99%

“…In order to highlight structure-function relations, we performed property-alignment in the ADAPTABLE web server [ 38 ]. It is important to point out that property alignment clusters sequences with specific activities (antibacterial in this case).…”

Section: Resultsmentioning

confidence: 99%

Antimicrobial Peptide K11 Selectively Recognizes Bacterial Biomimetic Membranes and Acts by Twisting Their Bilayers

et al. 2020

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“…Samarosporin I is the subfamily 2 peptaibol [33]. Its sequence is Ac-Phe-Aib-Aib-Aib-Val-Gly-Leu-Aib-Aib-Hyp-Gln-Iva-Hyp-Aib-Fol (Aib, Hyp, and Iva were defined above, while Ac and Fol, respectively, denote acetyl and phenylalaninol at the N-end and C-end of the peptide).…”

Section: Predictions For Samarosporin Imentioning

confidence: 99%

Monitoring the Site-Specific Solid-State NMR Data in Oligopeptides

Czernek

Brus

2020

IJMS

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Reliable values of the solid-state NMR (SSNMR) parameters together with precise structural data specific for a given amino acid site in an oligopeptide are needed for the proper interpretation of measurements aiming at an understanding of oligopeptides’ function. The periodic density functional theory (DFT)-based computations of geometries and SSNMR chemical shielding tensors (CSTs) of solids are shown to be accurate enough to support the SSNMR investigations of suitably chosen models of oriented samples of oligopeptides. This finding is based on a thorough comparison between the DFT and experimental data for a set of tripeptides with both 13Cα and 15Namid CSTs available from the single-crystal SSNMR measurements and covering the three most common secondary structural elements of polypeptides. Thus, the ground is laid for a quantitative description of local spectral parameters of crystalline oligopeptides, as demonstrated for the backbone 15Namid nuclei of samarosporin I, which is a pentadecapeptide (composed of five classical and ten nonproteinogenic amino acids) featuring a strong antimicrobial activity.

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“…To the best of our knowledge, LAMP2 ( 8 ), dbAMP ( 10 ), ADAPTABLE ( 15 ) and starPepDB ( 14 ) are the only general-type AMP databases to have come online since the time of our previous publication. ADAPTABLE is a web platform that aims to create families of property- and sequence-related peptides ( 15 ). starPepDB was created to solve the problem of data redundancy and duplication by standardizing it ( 14 ).…”

Section: Resultsmentioning

confidence: 99%

“…Between 2014 and 2016, the database was updated and expanded resulting in the release of the second version (DBAASP v2) with about 8000 entries ( 7 ). The expanded volume of data, including structural information, and new functionality made DBAASP v2 widely used in the research community, contributing to the development of several databases such as LAMP2 ( 8 ), dbAMP ( 10 ), PlantPepDB ( 13 ), starPepDB ( 14 ) and ADAPTABLE ( 15 ). DBAASP continues to expand through the addition of new content and additional user services, and from 2016 to 2019 the number of entries increased to >15 000.…”

Section: Introductionmentioning

confidence: 99%

DBAASP v3: database of antimicrobial/cytotoxic activity and structure of peptides as a resource for development of new therapeutics

Pirtskhalava¹,

Amstrong

Grigolava³

et al. 2020

Nucleic Acids Research

367

252

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The Database of Antimicrobial Activity and Structure of Peptides (DBAASP) is an open-access, comprehensive database containing information on amino acid sequences, chemical modifications, 3D structures, bioactivities and toxicities of peptides that possess antimicrobial properties. DBAASP is updated continuously, and at present, version 3.0 (DBAASP v3) contains >15 700 entries (8000 more than the previous version), including >14 500 monomers and nearly 400 homo- and hetero-multimers. Of the monomeric antimicrobial peptides (AMPs), >12 000 are synthetic, about 2700 are ribosomally synthesized, and about 170 are non-ribosomally synthesized. Approximately 3/4 of the entries were added after the initial release of the database in 2014 reflecting the recent sharp increase in interest in AMPs. Despite the increased interest, adoption of peptide antimicrobials in clinical practice is still limited as a consequence of several factors including side effects, problems with bioavailability and high production costs. To assist in developing and optimizing de novo peptides with desired biological activities, DBAASP offers several tools including a sophisticated multifactor analysis of relevant physicochemical properties. Furthermore, DBAASP has implemented a structure modelling pipeline that automates the setup, execution and upload of molecular dynamics (MD) simulations of database peptides. At present, >3200 peptides have been populated with MD trajectories and related analyses that are both viewable within the web browser and available for download. More than 400 DBAASP entries also have links to experimentally determined structures in the Protein Data Bank. DBAASP v3 is freely accessible at http://dbaasp.org.

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ADAPTABLE: a comprehensive web platform of antimicrobial peptides tailored to the user’s research

Abstract: ADAPTABLE is a webserver and database of antimicrobial peptides that uses sequence and property alignment to highlight their mode of action against the threat of resistance in medicine and agriculture.

Cited by 33 publications

References 88 publications

Antimicrobial Peptide K11 Selectively Recognizes Bacterial Biomimetic Membranes and Acts by Twisting Their Bilayers

Antimicrobial Peptide K11 Selectively Recognizes Bacterial Biomimetic Membranes and Acts by Twisting Their Bilayers

Monitoring the Site-Specific Solid-State NMR Data in Oligopeptides

DBAASP v3: database of antimicrobial/cytotoxic activity and structure of peptides as a resource for development of new therapeutics

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